------------------------------------------------------------------------
r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/Makefile
   A /trunk/samtools/bam_stat.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.2-1
 * added flagstat command

------------------------------------------------------------------------
r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/NEWS
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/samtools.1

Release SAMtools-0.1.2

------------------------------------------------------------------------
r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/indel_filter.pl

Script for filtering indel results

------------------------------------------------------------------------
r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/zoom2sam.pl

convert ZOOM to SAM

------------------------------------------------------------------------
r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines
Changed paths:
   A /trunk/samtools/misc/novo2sam.pl

add a script to convert novo alignment to SAM

------------------------------------------------------------------------
r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/ChangeLog
   M /trunk/samtools/ChangeLog.old
   M /trunk/samtools/samtools.1

update documentation and ChangeLog

------------------------------------------------------------------------
r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c

 * samtools-0.1.1-19
 * fixed a bug in "merge" command line

------------------------------------------------------------------------
r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/misc/Makefile
   A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108)
   M /trunk/samtools/misc/export2sam.pl
   A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108)
   A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108)
   A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108)

 * merge from branches/dev/
 * all future development will happen here

------------------------------------------------------------------------
r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines
Changed paths:
   M /trunk/samtools/COPYING
   M /trunk/samtools/ChangeLog
   A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108)
   M /trunk/samtools/Makefile
   A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108)
   M /trunk/samtools/bam.c
   M /trunk/samtools/bam.h
   M /trunk/samtools/bam_import.c
   M /trunk/samtools/bam_index.c
   M /trunk/samtools/bam_lpileup.c
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_maqcns.h
   A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108)
   M /trunk/samtools/bam_pileup.c
   M /trunk/samtools/bam_plcmd.c
   A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108)
   M /trunk/samtools/bam_sort.c
   M /trunk/samtools/bamtk.c
   M /trunk/samtools/bgzf.h
   M /trunk/samtools/examples/00README.txt
   A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108)
   D /trunk/samtools/examples/ex1.fa.fai
   M /trunk/samtools/examples/ex1.sam.gz
   M /trunk/samtools/faidx.c
   A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108)
   M /trunk/samtools/glf.h
   M /trunk/samtools/misc/Makefile
   M /trunk/samtools/misc/maq2sam.c
   M /trunk/samtools/razf.c
   M /trunk/samtools/source.dot

 * Merge from branches/dev/
 * all future development will happen here at trunk/

------------------------------------------------------------------------
r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines
Changed paths:
   M /trunk/samtools/bam_maqcns.c
   M /trunk/samtools/bam_tview.c

Fix problem with compiling without curses.

------------------------------------------------------------------------
r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /trunk/samtools (from /branches/dev/samtools:62)

Create trunk copy

------------------------------------------------------------------------
r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/NEWS
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

Release samtools-0.1.1

------------------------------------------------------------------------
r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines
Changed paths:
   M /branches/dev/samtools/bam_aux.c
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/razf.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-66
 * fixed a bug in razf.c: reset z_eof when razf_seek() is called
 * fixed a memory leak in parsing a region
 * changed pileup a little bit when -s is in use: output ^ and $
 * when a bam is not indexed, output more meaningful error message
 * fixed a bug in indexing for small alignment
 * fixed a bug in the viewer when we come to the end of a reference file
 * updated documentation
 * prepare to release 0.1.1

------------------------------------------------------------------------
r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/examples
   A /branches/dev/samtools/examples/00README.txt
   A /branches/dev/samtools/examples/ex1.fa
   A /branches/dev/samtools/examples/ex1.fa.fai
   A /branches/dev/samtools/examples/ex1.sam.gz

example

------------------------------------------------------------------------
r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/ChangeLog

update ChangeLog

------------------------------------------------------------------------
r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/misc/export2sam.pl

 * added comments
 * fixed several bugs 

------------------------------------------------------------------------
r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/misc/export2sam.pl

convert Export format to SAM; not thoroughly tested

------------------------------------------------------------------------
r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/source.dot

 * samtools-0.1.0-65
 * pileup: generate maq-like simple output
 * pileup: allow to output pileup at required sites
 * source.dot: source file relationship graph
 * tview: fixed a minor bug

------------------------------------------------------------------------
r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines
Changed paths:
   D /branches/dev/samtools/misc/all2sam.pl

remove all2sam.pl

------------------------------------------------------------------------
r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/COPYING
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/faidx.h
   M /branches/dev/samtools/khash.h
   M /branches/dev/samtools/kseq.h
   M /branches/dev/samtools/ksort.h
   M /branches/dev/samtools/samtools.1

Added copyright information and a bit more documentation. No code change.

------------------------------------------------------------------------
r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-64
 * improved efficiency of the indel caller for spliced alignments

------------------------------------------------------------------------
r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_aux.c
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-63
 * a bit code cleanup: reduce the dependency between source files

------------------------------------------------------------------------
r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-62
 * fixed a memory leak

------------------------------------------------------------------------
r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/ChangeLog
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/samtools.1

update documentation, ChangeLog and a comment

------------------------------------------------------------------------
r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_maqcns.h
   M /branches/dev/samtools/bam_pileup.c
   A /branches/dev/samtools/bam_plcmd.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-61
 * moved pileup command to a separate source file
 * added indel caller
 * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!)
 * updated documentation

------------------------------------------------------------------------
r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-60
 * fixed another bug in maqcns when there is a nearby deletion

------------------------------------------------------------------------
r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-59
 * pileup: outputing consensus is now optional
 * fixed a bug in glfgen. This bug also exists in maq's glfgen. However,
   I am not quite sure why the previous version may have problem.

------------------------------------------------------------------------
r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-58
 * add maq consensus to pileup. However, I will move this part to a new
   command as strictly speaking, consensus callin is not part of pileup,
   and imposing it would make it harder to generate for other language
   bindings.

------------------------------------------------------------------------
r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bgzf.c

Fix bug in tell() after reads that consume to the exact end of a block.

------------------------------------------------------------------------
r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/samtools.1

update manual

------------------------------------------------------------------------
r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-57
 * fixed a bug in parser when there is auxiliary fields
 * made the parser a bit more robust

------------------------------------------------------------------------
r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/bgzf.c

 * samtools-0.1.0-56
 * fixed a bug in bgzf (only reading is affected)
 * fixed a typo in bam_index.c
 * in bam_index.c, check potential bugs in the underlying I/O library

------------------------------------------------------------------------
r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/samtools.1

update manual

------------------------------------------------------------------------
r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-55
 * tried to make pileup work with clipping (previously not), though NOT tested
 * removed -v from pileup
 * made pileup take the reference sequence

------------------------------------------------------------------------
r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-54
 * in parser, recognize "=", rather than ",", as a match
 * in parser, correctl parse "=" at the MRNM field.

------------------------------------------------------------------------
r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/maq2sam.c

fixed a bug in handling maq flag 64 and 192

------------------------------------------------------------------------
r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/md5fa.c

also calculate unordered md5sum check

------------------------------------------------------------------------
r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/md5fa.c

fixed a minor bug when there are space in the sequence

------------------------------------------------------------------------
r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/md5fa.c

fixed a potential memory leak

------------------------------------------------------------------------
r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c

 * fixed a bug in import: bin is wrongly calculated

------------------------------------------------------------------------
r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/misc/all2sam.pl

nothing, really

------------------------------------------------------------------------
r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/kseq.h
   M /branches/dev/samtools/misc/Makefile
   A /branches/dev/samtools/misc/md5.c
   A /branches/dev/samtools/misc/md5.h
   A /branches/dev/samtools/misc/md5fa.c

 * fixed two warnings in kseq.h
 * added md5sum utilities

------------------------------------------------------------------------
r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/kseq.h
   D /branches/dev/samtools/kstream.h

 * samtools-0.1.0-52
 * replace kstream with kseq. kseq is a superset of kstream. I need the
   extra functions in kseq.h.
 * also compile stand-alone faidx

------------------------------------------------------------------------
r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_sort.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-51
 * sorting by read names is available

------------------------------------------------------------------------
r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bam_sort.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/misc/maq2sam.c

 * samtools-0.1.0-50
 * format change to meet the latest specification

------------------------------------------------------------------------
r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/misc/maq2sam.c

 * minor change in maqcns: special care when n==0
 * change maq2sam to meet the latest specification

------------------------------------------------------------------------
r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/razf.c
   M /branches/dev/samtools/razf.h

considerable code clean up in razf

------------------------------------------------------------------------
r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/ChangeLog
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/faidx.c

make RAZF optional in faidx.c

------------------------------------------------------------------------
r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/bam_aux.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-49
 * added routines for retrieving aux data, NOT TESTED YET!

------------------------------------------------------------------------
r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines
Changed paths:
   M /branches/dev/samtools/bam.c
   M /branches/dev/samtools/bam_import.c
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/bgzf.c
   M /branches/dev/samtools/samtools.1

 * samtools-0.1.0-48
 * bgzf: fixed a potential integer overflow on 32-it machines
 * maqcns: set the minimum combined quality as 0
 * supporting hex strings

------------------------------------------------------------------------
r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/bam_maqcns.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-47
 * fixed the bug in maqcns

------------------------------------------------------------------------
r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   A /branches/dev/samtools/bam_maqcns.c
   A /branches/dev/samtools/bam_maqcns.h
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/glf.h

 * samtools-0.1.0-46
 * add MAQ consensus caller, currently BUGGY!

------------------------------------------------------------------------
r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_pileup.c
   M /branches/dev/samtools/bam_tview.c
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-45
 * tview: display padded alignment (but not P operation)
 * better coordinates and reference sequence

------------------------------------------------------------------------
r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/ChangeLog

new ChangeLog

------------------------------------------------------------------------
r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines
Changed paths:
   D /branches/dev/samtools/ChangeLog
   A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6)

Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from
the log of my personal SVN repository.

------------------------------------------------------------------------
r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/bgzf.c

 * samtools-0.1.0-44
 * declare fseeko and ftello as some Linux may not do this by default and
   missing these declarations will make bgzf buggy
 * get rid of some harmless warings
 * use BGZF by default, now

------------------------------------------------------------------------
r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bam_index.c
   M /branches/dev/samtools/bamtk.c
   M /branches/dev/samtools/razf.c

 * samtools-0.1.0-43
 * fixed a bug in razf_read()
 * give more warnings when the file is truncated (or due to bugs in I/O library)

------------------------------------------------------------------------
r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bgzf.c

fixed a bug in bgzf.c at the end of the file

------------------------------------------------------------------------
r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines
Changed paths:
   M /branches/dev/samtools/bamtk.c

 * samtools-0.1.0-42
 * a lot happened to RAZF, although samtools itself is untouched. Better
   also update the version number anyway to avoid confusion

------------------------------------------------------------------------
r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/razf.c

a change from Jue, but I think it should not matter

------------------------------------------------------------------------
r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines
Changed paths:
   M /branches/dev/samtools/razf.c

fixed a potential bug in razf. However, it seems still buggy, just
rarely happens, very rarely.

------------------------------------------------------------------------
r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/razf.c

fixed a bug in razf, with the help of Jue

------------------------------------------------------------------------
r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/bam_index.c

remove a comment

------------------------------------------------------------------------
r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines
Changed paths:
   M /branches/dev/samtools/Makefile
   M /branches/dev/samtools/bam.h
   M /branches/dev/samtools/razf.c
   M /branches/dev/samtools/razf.h

 * Jue has updated razf to realize Bob's scheme

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r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools/samtools.1

the manual page

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r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines
Changed paths:
   A /branches/dev/samtools/ChangeLog
   A /branches/dev/samtools/Makefile
   A /branches/dev/samtools/bam.c
   A /branches/dev/samtools/bam.h
   A /branches/dev/samtools/bam_aux.c
   A /branches/dev/samtools/bam_endian.h
   A /branches/dev/samtools/bam_import.c
   A /branches/dev/samtools/bam_index.c
   A /branches/dev/samtools/bam_lpileup.c
   A /branches/dev/samtools/bam_pileup.c
   A /branches/dev/samtools/bam_sort.c
   A /branches/dev/samtools/bam_tview.c
   A /branches/dev/samtools/bamtk.c
   A /branches/dev/samtools/bgzf.c
   A /branches/dev/samtools/bgzf.h
   A /branches/dev/samtools/bgzip.c
   A /branches/dev/samtools/faidx.c
   A /branches/dev/samtools/faidx.h
   A /branches/dev/samtools/khash.h
   A /branches/dev/samtools/ksort.h
   A /branches/dev/samtools/kstream.h
   A /branches/dev/samtools/misc
   A /branches/dev/samtools/misc/Makefile
   A /branches/dev/samtools/misc/all2sam.pl
   A /branches/dev/samtools/misc/maq2sam.c
   A /branches/dev/samtools/razf.c
   A /branches/dev/samtools/razf.h
   A /branches/dev/samtools/razip.c
   A /branches/dev/samtools/zutil.h

The initial version of samtools, replicated from my local SVN repository.
The current version is: 0.1.0-42. All future development will happen here.

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r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines
Changed paths:
   A /branches/dev/samtools

samtools (C version)

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